Its last known location was off the North Carolina coast in the “Graveyard of the Atlantic.” President Lincoln was among those who saw it before it vanished.

The Alligator was the U.S. Navy’s first submarine.

If you haven’t heard of this mysterious craft, you are in good company. You won’t find much, if anything, about it in history books. But thanks to a dedicated team of naval historians, maritime archaeologists, oceanographers, meteorologists, students, and others, the story of Alligator will not be lost to the ages.

Today, few are aware of the Alligator and its place in history. Until recently, its existence was news even to lifelong U.S. Navy submariners, including Rear Adm. Jay Cohen, currently the chief of naval research.

“I had never heard of the Alligator. I had never read about or seen a reference to itnothing,” said Cohen.

It was Cohen’s wife who alerted him to it after reading an article about the sub in a Civil War magazine. Cohen was stunned. Most history books cite the USS Holland, launched in 1897, as the Navy’s first sub.

Eager to delve deeper into the Alligator’s story, Cohen shared the article with Daniel J. Basta, director of NOAA’s National Marine Sanctuary Program, and world renowned ocean explorer Dr. Robert Ballard, who discovered the Titanic. The admiral knew they would immediately grasp the significance of the submarine to American history and might be in a position to aid in the search for clues into the history and possible location of the long-lost sub.

After enlisting the help of naval historian, artist, and retired submariner James Christley and Navy Cmdr. Rich Poole, they soon learned that the Alligator was something right out of Jules Verne’s 20,000 Leagues Under the Sea. In fact, according to one translation of that novel, Villeroi was Verne’s math teacher.

Built to counter the threat of Confederate ironclads, the green, oar-propelled sub was a vessel like no other. Among its most notable features was an airlock designed to allow a diver to exit the vessel while submerged and place an explosive charge on an enemy ship. The Alligator’s design also included an air purification system. Both are standard components of modern submarines.

Following its launch from a Philadelphia shipyard in 1862, the Alligator was tasked with destroying bridges crossing the Appomattox River and clearing obstructions in the James River in Virginia. But the Alligator would never get the chance to prove itself in battle.

After arriving in the combat zone, the waters of the James and Appomattox proved too shallow to allow the sub to submerge. The Alligator was also less maneuverable than expected.

Fearing that it could be captured by the Confederacy, the Alligator was withdrawn and towed to the Navy Yard in Washington, D.C., where it was refitted with a hand-cranked screw propeller. President Lincoln himself witnessed a demonstration of the “improved” vessel.

After declaring that the Alligator was ready for action, Rear Adm. Samuel Dupont ordered the sub to Charleston, S.C., in March 1863. It would be a fateful journey.

While heading south along the North Carolina coast, the Alligator and its tow vessel, the USS Sumpter, encountered a storm so fierce that the Sumpter’s crew, facing the loss of their own ship, was forced to cut the unmanned submarine loose. The Union sub was never seen again.

“We don’t know what happened to the Alligator after its towline was cut,” said Basta, whose program protects and manages the famed Civil War ironclad USS Monitor and other shipwrecks. “Did it sink right away? Did it float for days and then sink? Did it wash up on a beach somewhere?”

To help answer those questions, Basta enlisted the assistance of faculty and students at the U.S. Naval Academy (USNA). After all, three decades earlier, naval academy instructors and midshipmen had aided in the successful search for the Monitor. The USNA team formulated a number of theories about the Alligator’s fate based on the best information available.

Basta also looked internally for help. He knew that the key to success was learning more the Alligator and the man who invented it, French immigrant and self-described “natural genius” Brutus de Villeroi. Immediately, he thought of NMSP’s national partnership coordinator, Catherine Marzin, who hails from Villeroi’s native France. Knowing that Marzin was already planning to visit relatives in France, Basta presented her with a challenge: Find the blueprints to the Alligator!

Marzin’s search for information about Villeroi and the sub led her to the French naval archives outside Paris. Sure enough, they had a file, or, rather, a box. It contained a complete set of original drawings of the Alligator. They are the only blueprints of the submarine found to date.

With the drawings were a number of hand-written letters exchanged by Villeroi and the French government. The letters document Villeroi’s repeated but unsuccessful attempts to persuade his own country to purchase his submarine designs.

The newly “discovered” blueprints are already helping to refine theories about the vessel’s fate.

“The blueprints provide information that we can use to calculate how quickly the Alligator may have flooded and how fast it may have been going when it hit the seafloor,” said the sanctuary program’s Michiko Martin, who was one of the naval academy instructors involved in the Alligator Project before joining NOAA in the fall of 2002.

The blueprints and other recent findings by the project team generated a lot of enthusiasm in October 2003 at the first-ever symposium about the Alligator. Sponsored by ONR and NOAA and held at the Submarine Force Museum in Groton, Conn., the meeting sparked discussion about the possibility of locating and recovering the historically significant vessel.

Cohen argued that the hunt for the Alligator would be an excellent test of our ability to find a relatively small object on the seafloor “in an intelligent way over a reasonable period of time and at a reasonable cost.”

In the age of ultra-quiet diesel submarines and heightened concerns about the security of our ports and near-shore waters, it’s the potential deployment of small, inexpensive submerged weapons that keeps Cohen awake at night. “But if we can find the Alligator, we can find anything.”

The consensus among the symposium’s participants was that the hunt itself is as important as actually recovering the craft. Everyone saw the potential for raising awareness of the historically important vessel and renewing public interest in science, technology and history.

“The search for [this] 140-year old vessel can lead us to develop new means of protecting our nation and our environment,” said Navy and Marine Living History Association President Chuck Veit, who attended the Groton meeting. Veit believes so strongly in what the Alligator can tell us that his organization has launched its own Web site devoted to the sub.

For his part, Jim Christley wants “the Alligator and the men who designed, built and sailed in her take their rightful place in naval history alongside the [early submarines] Turtle, H.L. Hunley and USS Holland.”

“Whether we find the Alligator or not, the hunt for the Alligator will help us move ocean science and exploration forward,” said symposium participant Capt. Craig McLean, a NOAA Corps officer. “We also will engage, and hopefully inspire, more than a few budding scientists and historians along the way.” [Paintings by Jim Christley]